Elissa Lei, Ph.D.

Research Goal

The work performed in my laboratory will help determine how the 3-dimensional organization of DNA within each cell affects cellular function and identity throughout development.

Current Research

Importance of genome organization and our approaches

It has become increasingly apparent that proper control of gene expression requires complex organization of DNA at the level of chromatin. We study how genome organization contributes to regulation of gene expression, which ultimately controls how a single genome can give rise to a myriad of distinct cell types with different functions and properties. Our primary model system is Drosophila melanogaster, which harbors powerful genetics, biochemistry, imaging, and genomics approaches as well as a number of well-characterized cell lines derived from a variety of tissues and stages of development. We also utilize mouse and silkworm moth models to study conserved aspects of genome organization.

Relevance of chromatin insulators

Chromatin insulators are DNA-protein complexes that influence gene expression by establishing chromatin domains subject to distinct transcriptional controls, likely through alteration of their spatial organization. Insulators are required for the formation of topologically associating domains (TADs), and on a local scale, insulators enforce the strict specific and temporal expression of loci with complex enhancer and/or promoter configuration. Examples include metazoan Hox genes, master regulators of body segmentation, and the vertebrate beta-globin locus, which changes in expression during erythroid development. Loss of insulator activity can result in substantial positive or negative changes in gene expression, culminating in disease, defects in development, and/or lethality. For example, deletion of insulator binding sites at the H19/IGF2 imprinting center have been implicated in Beckwith-Wiedemann syndrome and Wilms’ Tumor. Moreover, recent studies have shown that loss of insulator activity in IDH1 mutant gliomas and T cell acute lymphoblastic leukemias leads to disruption of boundaries between chromatin domains and subsequent oncogene activation.

Tissue-specific regulation of insulator activity and antagonism of chromatin looping

Drosophila harbors the largest diversity of known chromatin insulator complexes. We identified two novel, tissue-specific negative regulators of gypsy insulator function that affect both enhancer blocking and barrier activities. Shep can bind directly to Su(Hw) as well as another core component of the gypsy insulator complex, potentially competing with inter- or intra-insulator complex interactions and thereby neutralizing insulator activity. Shep is required for neuronal remodeling during development and is highly enriched in the CNS, perhaps serving to negatively regulate insulator function in these cell types to promote CNS-specific gene expression programs. We recently found that Shep can antagonize enhancer-promoter looping of one of its downstream transcriptional targets in a temporal manner. Shep harbors two highly conserved RNA recognition motifs (RRMs), and genetic evidence points to a functional relationship between its RNA-binding capability and insulator function. In contrast, Rump, which contains 3 RRMs, antagonizes gypsy insulator activity in tissues outside of the CNS.

RNA-dependent insulator function

Using RNA immunoprecipitation followed by deep sequencing (RIP-seq), we made the striking finding that certain mRNAs, including that encoding Su(Hw) itself, associate stably with gypsy insulator complexes. Expression of untranslatable versions of these mRNAs alters insulator body localization and promotes insulator activity. We speculate that these mRNAs also harbor a noncoding function, such as acting as a scaffold for insulator complexes at specific subnuclear locations. We recently identified a novel RNA-binding protein, Isha, that binds to the su(Hw) mRNA and is required for gypsy insulator function.

(This work was highlighted in Editors' Choice, Riddihough G. Noncoding mRNAs. Science, (341)6149: 938, 2013.)

Link: https://www.science.org/doi/10.1126/science.2013.341.6149.twil

Research in Plain Language

Each cell within the body contains the identical genetic information, but the complement of genes that are active at any given time is a critical factor in determining the type of cell (i.e. kidney, lung, heart) and its specific function within a particular tissue. All of the genetic information is contained within the DNA, and if the DNA were stretched end to end, it would extend 2 meters. Therefore, the DNA must be tightly packaged in order to fit within the cell. At the same time, the genes within the DNA must be kept accessible to the cellular machinery in order to be read as the genetic blueprint to produce RNA and proteins, the actual workhorses of the cell. The DNA is wrapped around a variety of proteins that help compact and organize its overall structure. One such complex of DNA-bound protein is called a chromatin insulator. With respect to the genetic blueprint, chromatin insulators function similarly to punctuation within a paragraph, in order to help subdivide otherwise incoherent strings of words into sentences and to logically connect related phrases.

My laboratory studies how chromatin insulators function and how they help control which genes are active. Studying how chromatin insulators work helps improve our understanding of how cells develop and give rise to different tissues. When chromatin insulators malfunction, disease can result. In fact, a single cell cannot survive without the activity of chromatin insulators.

Since chromatin insulators exist and function similarly in most multicellular animal organisms, we use the relatively simple fruit fly Drosophila as a model organism. Working with Drosophila is advantageous to doing experiments in mammals because of their much faster generation time and ease of use in genetic experiments. The Drosophila system is also extremely powerful for biochemistry and cell biology techniques, and the Drosophila genome has the largest diversity of known chromatin insulator proteins.